Re: Python based tool for analysis of DCD trajectories

From: Brian Radak (brian.radak_at_gmail.com)
Date: Fri Mar 09 2018 - 08:41:16 CST

You are definitely correct in eschewing ASCII formats like XYZ for
large-scale analysis.

VMD is generally the recommended tool for trajectory analysis, substituting
a Tcl interface for Python. I understand that a lot of new users find this
a bit annoying since Python seems to be the tool of choice these days (I
certainly had the same opinion when I started out), but spending time to
learn Tcl can be advantageous and satisfying for a number of reasons (not
exhaustive):

1) it can naturally interface with the VMD back-end (vectorized and GPU
accelerated measurements, natural language selection, etc)
2) it has very good support for Tk and thus can be fairly easily converted
to a GUI plugin for yourself and/or posterity
3) Tcl is generally more portable than Python, especially if you want to
work with data remotely on supercomputers

Python still might be a good tool for your purposes, but VMD and Tcl may
also be an excellent choice.

Cheers,
BKR

On Fri, Mar 9, 2018 at 1:52 AM, Haohao Fu <fhh2626_at_gmail.com> wrote:

> you can use MDtraj(http://mdtraj.org/1.9.0/), MDanalysis(https://www.
> mdanalysis.org/) or prody(http://prody.csb.pitt.edu/) to do such things.
>
> Haohao
>
> 2018-03-09 13:46 GMT+08:00 Harish Srinivasan <harishlglk1992_at_gmail.com>:
>
>> I am using NAMD to simulate various systems like bilayer, micelles,
>> eutectic solvents etc. Most of my analysis is using the trajectories of the
>> system (i.e. x,y,z coordinates of the atom). So far I have been using
>> catdcd to convert my dcd trajectory files to xyz format and then use it for
>> further analysis.
>>
>> Is there any particular tool (preferably python based) that can in
>> principle allow me to get the (x,y,z) coordinates from DCD file based on,
>> different selections of residues/segments/atom_number etc?
>>
>> Thank you
>> Harish
>>
>
>

This archive was generated by hypermail 2.1.6 : Thu Sep 19 2019 - 23:19:29 CDT